Iron in the structure of Crystal Structure of Non-Symbiotic Plant Hemoglobin From Rice (pdb 1d8u)

The binding sites of Iron atom in the structure of Crystal Structure of Non-Symbiotic Plant Hemoglobin From Rice (pdb code 1d8u). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1d8u structure was solved by M.HARGROVE, E.A.BRUCKER, B.STEC, J.S.OLSON, G.N.PHILLIPS JR., with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

Resolution (A)

50.0-2.4

Space group

P3121

a (A)

126.800

b (A)

126.800

c (A)

55.500

alpha (°)

90.00

beta (°)

90.00

gamma (°)

120.00

Rfactor (%)

20.8

Rfree (%)

26.1

Iron Binding Sites:

Iron binding site 1 out of 2 in 1d8u

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1d8u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: His73, A: His108, A: Hem166,

conact list:

Atom

Atom

Distance (A)

Fe

NE2 A:His73

2.08

Fe

ND1 A:His73

4.24

Fe

CD2 A:His73

3.05

Fe

CE1 A:His73

3.12

Fe

CG A:His73

4.20

Fe

NE2 A:His108

2.08

Fe

ND1 A:His108

4.23

Fe

CD2 A:His108

3.05

Fe

CE1 A:His108

3.11

Fe

CG A:His108

4.19

Fe

C2D A:Hem166

4.23

Fe

NC A:Hem166

1.98

Fe

CHB A:Hem166

3.41

Fe

CHC A:Hem166

3.40

Fe

C3D A:Hem166

4.23

Fe

NA A:Hem166

1.98

Fe

CHA A:Hem166

3.39

Fe

C2A A:Hem166

4.27

Fe

C1D A:Hem166

3.01

Fe

C4A A:Hem166

3.03

Fe

C4B A:Hem166

3.02

Fe

C3A A:Hem166

4.27

Fe

C4C A:Hem166

3.02

Fe

C2B A:Hem166

4.24

Fe

C1C A:Hem166

3.02

Fe

C2C A:Hem166

4.26

Fe

ND A:Hem166

1.96

Fe

CHD A:Hem166

3.39

Fe

C1B A:Hem166

3.02

Fe

NB A:Hem166

1.97

Fe

FE A:Hem166

0.00

Fe

C3C A:Hem166

4.25

Fe

C3B A:Hem166

4.25

Fe

C4D A:Hem166

3.00

Fe

C1A A:Hem166

3.03

interactive model:

Iron binding site 2 out of 2 in 1d8u

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1d8u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: B: His73, B: His108, B: Hem166,